Biowulf High Performance Computing at the NIH
Pyclone on HPC

PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples. The input data for PyClone consists of a set read counts from a deep sequencing experiment, the copy number of the genomic region containing the mutation and an estimate of tumour content.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=10g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pyclone
[user@cn3144 ~]$ cp -r /usr/local/apps/pyclone/examples /data/$USER
[user@cn3144 ~]$ cd /data/$USER/examples/mixing/tsv
[user@cn3144 ~]$ PyClone run_analysis_pipeline --in_files SRR385939.tsv SRR385940.tsv SRR385941.tsv --working_dir pyclone_analysis
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

This will create a directory pyclone_analysis. After the command completes the directory will contain several folders and the file config.yaml:

The contents of these folders are as follows:

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load pyclone
PyClone run_analysis_pipeline --in_files SRR385939.tsv SRR385940.tsv SRR385941.tsv --working_dir pyclone_analysis

Submit this job using the Slurm sbatch command.

sbatch [--mem=#]
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. job.swarm). For example:

cd dir1;PyClone ...
cd dir2;PyClone ...
cd dir3;PyClone ...
cd dir4;PyClone ...

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module pyclone
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm